Aside

Jacob Arie

Contact Info

Skills

Languages

  • Fluent Dutch (Native language)
  • Fluent English (C2 level)
  • Basic swedish reading level (A2 reading level)

Programming languages

  • R
  • Python
  • Bash
  • SLURM

Main

Jacob Arie van Diermen

MSc, Research assistant

Profile

Personal profile

N/A

N/A

N/A

I am an enthusiastic aspiring researcher that wants to further my career in the field of bioinformatics. My ambition is to analyze large biological datasets with the computational skills developed during my bachelor’s and master’s education to answer exciting new biological questions. I aspire to develop my skills in analyzing, visualizing and interpreting these large datasets, which is helped by my extensive biological background

Education

Utrecht university, Graduate School of Life Sciences

MSc Molecular and Cellular life sciences (MCLS), specialization Biophysics & Molecular Imaging, Bioinformatics minor profile

Utrecht, The Netherlands

2023 - 2020

Final grade: 8.02/10

Bioinformatics minor profile

  • Thesis: Comparative genomics approach finds DNA-repair and immune-related genes in the regenerative African spiny mouse

Major research project

  • Thesis: Characterization of CSPP1 interaction with microtubules in cells

Utrecht university, Department of Biology

BSc in Biology

Utrecht, The Netherlands

2020 - 2017

graduated with honors (cum laude)

Final grade: 8.14/10

Bachelor thesis: Promising molecular targets for therapeutic intervention in Alzheimer’s disease

Research Experience

Research assistant

Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)

Solna, Sweden

Current - 2023/07


  • Continuation of the research project as a research assistant
  • Preparing and writing a manuscript for publication
  • Presenting data at lab meetings
  • Creating Docker and Singularity containers for the positive selection pipeline
  • Working with positive selection tools like HyPhy MEME. HyPhy aBSREL and PAML codeml
  • Experience working with the Linux operating system (Ubuntu, Pop!_OS)
  • Writing parallelized bash and R scripts for the positive selection pipeline
  • Accessing and working with publicly available single-cell datasets form GTEX

Teaching assistant

Utrecht university, Department of Biology

Utrecht, The Netherlands

2023/05 - 2023/02


Teaching assistant for the course Kwantitatieve biologie (B-B1KWBI20), a quantitative biology course for first year biology students.

Research intern

Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)

Solna, Sweden

2023/03 - 2022/05


  • Bioinformatic analysis
  • Comparative genomics
  • Working with positive selection tools like HyPhy MEME and HyPhy aBSREL
  • Working with genomics data
  • Gene ontology analyses
  • Cytoscape and STRINGdb network analysis
  • Adept programming experience in R, Python and bash
  • Experience with High performance computing in a SLURM environment
  • Construction of a custom positive selection analysis pipeline for a large number of multiple sequence alignments
  • Experience with Git and github
  • Presenting and writing skills
  • Creation of a scientific poster for a conference
  • Creation of data visualizations using R

Research intern

Utrecht university, Cell biology, neurobiology and biophysics, Anna Akhmanova Group (Cellular dynamics)

Utrecht, The Netherlands

2022/03 - 2021/01


  • Extensive cell culture with mammalian adherent cell lines (COS7, RPE, HeLa)
  • Molecular cloning with SNAPtag, LEXY, PA-GFP, EB3 constructs
  • Transfections
  • Transformation of E.coli
  • Western blots (Semi-dry blotting)
  • PCR
  • Immunofluorescence staining
  • Fluorescence microscopy
  • Expansion microscopy (STED)
  • Live-cell imaging (spinning disk, TIRF)
  • Experiment planning
  • Presenting data
  • General lab skills

Additional skills

Software skills

N/A

N/A

  • STRING network analysis
  • gene ontology analysis
  • Cytoscape
  • Docker
  • Singularity
  • Git
  • Github
  • Rsudio
  • Anaconda
  • HyPhy (aBSREL, MEME)
  • PAML codeml
  • GraphPad Prism 8
  • Fiji/ ImageJ
  • Biorender

Talks and conferences

Genetic deconvolution of regenerative phenotypes in Acomys cahirinus

Tissue and Motion Conference 2022 (Poster)

Djurhamn, Sweden

2022

Aditya Singh, Sebastian A. Lewandowski, Katarina Tengvall, Michael Dong, Kerstin Lindblad-Toh

Recognition

Theme winner (Energy) Sustainable campus challenge 2020

Utrecht Challenge Alliance

Utrecht, The Netherlands

2020


I participated in the sustainable campus challenge 2020 organized by the Utrecht challenge alliance. This is a partnership for open innovation to find regional solutions to social issues in cooperation between companies, public organisations, governments and educational institutions. We were tasked to come up with a concept to reduce the energy usage of student housing and came up with a concept that rewards students for their sustainable behaviour. Our concept was chosen as the best concept to reduce student energy usage.

Latin honors (Cum laude) for BSc in Biology

Utrecht university, Department of Biology

Utrecht, The Netherlands

2020